Research Article

Systems proteomics of liver mitochondria function

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Science  10 Jun 2016:
Vol. 352, Issue 6291, aad0189
DOI: 10.1126/science.aad0189

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Expanded proteomic analysis of metabolism

Combined analysis of large data sets characterizing genes, transcripts, and proteins can elucidate biological functions and disease processes. Williams et al. report an exceptionally detailed characterization of mitochondrial function in a genetic reference panel of recombinant inbred mice. They measured the metabolic function of nearly 400 mice under various environmental conditions and collected detailed quantitative information from livers of the animals on over 25,000 transcripts. These data were integrated with quantitation of over 2500 proteins and nearly 1000 metabolites. Such analysis showed a frequent lack of correlation of transcript and protein abundance, enabled the identification of genomic variants of mitochondrial enzymes that caused inborn errors in metabolism, and revealed two genes that appear to function in cholesterol metabolism.

Science, this issue p. 10.1126/science.aad0189

Structured Abstract


Over the past two decades, continuous improvements in “omics” technologies have driven an ever-greater capacity to define the relationships between genetics, molecular pathways, and overall phenotypes. Despite this progress, the majority of genetic factors influencing complex traits remain unknown. This is exemplified by mitochondrial supercomplex assembly, a critical component of the electron transport chain, which remains poorly characterized. Recent advances in mass spectrometry have expanded the scope and reliability of proteomics and metabolomics measurements. These tools are now capable of identifying thousands of factors driving diverse molecular pathways, their mechanisms, and consequent phenotypes and thus substantially contribute toward the understanding of complex systems.


Genome-wide association studies (GWAS) have revealed many causal loci associated with specific phenotypes, yet the identification of such genetic variants has been generally insufficient to elucidate the molecular mechanisms linking these genetic variants with specific phenotypes. A multitude of control mechanisms differentially affect the cellular concentrations of different classes of biomolecules. Therefore, the identification of the causal mechanisms underlying complex trait variation requires quantitative and comprehensive measurements of multiple layers of data—principally of transcripts, proteins, and metabolites and the integration of the resulting data. Recent technological developments now support such multiple layers of measurements with a high degree of reproducibility across diverse sample or patient cohorts. In this study, we applied a multilayered approach to analyze metabolic phenotypes associated with mitochondrial metabolism.


We profiled metabolic fitness in 386 individuals from 80 cohorts of the BXD mouse genetic reference population across two environmental states. Specifically, this extensive phenotyping program included the analysis of metabolism, mitochondrial function, and cardiovascular function. To understand the variation in these phenotypes, we quantified multiple, detailed layers of systems-scale measurements in the livers of the entire population: the transcriptome (25,136 transcripts), proteome (2622 proteins), and metabolome (981 metabolites). Together with full genomic coverage of the BXDs, these layers provide a comprehensive view on overall variances induced by genetics and environment regarding metabolic activity and mitochondrial function in the BXDs. Among the 2600 transcript-protein pairs identified, 85% of observed quantitative trait loci uniquely influenced either the transcript or protein level. The transomic integration of molecular data established multiple causal links between genotype and phenotype that could not be characterized by any individual data set. Examples include the link between D2HGDH protein and the metabolite D-2-hydroxyglutarate, the BCKDHA protein mapping to the gene Bckdhb, the identification of two isoforms of ECI2, and mapping mitochondrial supercomplex assembly to the protein COX7A2L. These respective measured variants in these mitochondrial proteins were in turn associated with varied complex metabolic phenotypes, such as heart rate, cholesterol synthesis, and branched-chain amino acid metabolism. Of note, our transomics approach clarified the contested role of COX7A2L in mitochondrial supercomplex formation and identified and validated Echdc1 and Mmab as involved in the cholesterol pathway.


Overall, these findings indicate that data generated by next-generation proteomics and metabolomics techniques have reached a quality and scope to complement transcriptomics, genomics, and phenomics for transomic analyses of complex traits. Using mitochondria as a case in point, we show that the integrated analysis of these systems provides more insights into the emergence of the observed phenotypes than any layer can by itself, highlighting the complementarity of a multilayered approach. The increasing implementation of these omics technologies as complements, rather than as replacements, will together move us forward in the integrative analysis of complex traits.

Model of the transomics analysis.

A transomics approach was taken to analyze genetic and environmental variation in metabolic and mitochondrial phenotypes by measuring five distinct layers of biology in a diverse population of BXD mice. The combined analysis of all layers together provides additional information not yielded by any single omics approach.


Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its protein’s activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics—a combination moving us forward in complex trait analysis.

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